#!/bin/bash

echo Converts ALL *.xyz files in the current folder to *.pdb using VMD
echo Usage:   ./xyzpdb  [command to run vmd]
echo Default:  command to run vmd=vmd

if [ $# -lt 1 ];
then
	vmd=vmd #/opt/local/vmd-1.8.7beta5/bin/vmd
else
	vmd=$1
fi

for i in $(ls *.xyz)
do
    name=${i:0:${#i}-4}
    ./gen_vmd_script $name > xyz2pdb.vmd
    $vmd -e xyz2pdb.vmd -eofexit -dispdev none
done

